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Add Erics spheroid config for reference

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Paul Brinkmeier 2024-02-05 13:28:47 +01:00
parent fb187dd3c5
commit 9d7b0028a6
2 changed files with 160 additions and 0 deletions
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116
experiments/configs/spheroid/config.json Normal file
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{
"Comments": ["Celltype Usage", "0 Not Used", "1-5 Solids for blood vessels / ECM", "6 Liquid ", "7 Apoptotic cell Type ", "8 Basic Non Dividing Cell type (surrounding)", "9 Cancer"],
"Application": "Cells",
"CellsInSilico": {
"ecmdegradation": {
"enabled": "false",
"steps": 99999,
"stochastic": "true",
"probability": 0.5
},
"energyfunctions": ["Volume00", "Surface01", "Motility00", "Adhesion01", "DynamicECM00"],
"liquid": 6,
"volume": {
"default": {
"storage": "const",
"value": 500
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 7.5, 7.5, 7.5],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0]
},
"surface": {
"default": {
"storage": "const",
"value": 400
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 5.625, 5.625, 1],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0, 0]
},
"adhesion": {
"matrix": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 450],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 450, 0, 0, 0, 0, 0, 0, 0, 50]
]
},
"temperature": 50,
"division": {
"enabled": "true",
"condition": ["", "", "", "", "", "", "", "", "", "( volume >= 0.9 * volume0 ) & ( rnd() <= 0.00001 ) & generation < 1"]
},
"centerofmass": {
"steps": 1
},
"signaling": {
"enabled": false
},
"orientation": {
"enabled": true,
"motility": "persistentRandomWalk",
"persistenceMagnitude": 0.0,
"recalculationtime": 200,
"motilityamount": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
},
"visitor": {
"stepwidth": 10,
"checkerboard": "01"
},
"cleaner": {
"killDistance": 20
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 100,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,
"deltat": 0.1,
"eta": 0.25,
"k0": 0.1,
"k1": 0.1,
"c": 4,
"alpha": 2,
"d": 0.3,
"phi": 1
}
},
"Geometry": {
"blockcount": [8, 8, 6],
"blocksize": [50, 50, 67]
},
"Settings": {
"randomseed": 0,
"timesteps": 100
},
"WriteActions": ["CellInfo"],
"Writers": {
"CellInfo": {
"field": "",
"groupsize": 0,
"steps": 1,
"writer": "CellInfo"
},
"ParallelVTK_Cells": {
"field": "cells",
"outputtype": "UInt32",
"printhints": false,
"steps": 1,
"writer": "ParallelVtkImage"
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 1
}
},
"Include": "config_filling_1.json"
}

44
experiments/configs/spheroid/config_filling_1.json Normal file
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{
"DefineFunctions": [
"r_angle()=360*rnd()",
"r_size()=400*rnd()"
],
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[0, 0, 0],
[399, 399, 401]
],
"value": 0,
"celltype": 0
},
{
"shape": "sphere",
"pattern": "voronoi",
"count": 5500,
"radius": 75,
"center": [
200,
200,
200
],
"box": [
[
110,
110,
110
],
[
290,
290,
290
]
],
"celltype": 9
}
]
}
}